Methamphetamine regioisomers can be differentiated with the use of gas chromatography/MS. The findings of this study show that the analyst can make these identifications by MS instead of by derivitization techniques, gas chromatography-infrared, or chromatographic separations. This study developed a total fragmentation analysis of methamphetamine based on fundamental principles of cleavage, rearrangement, and secondary decomposition, supported by the available experimental data. The proposed analysis may be used as a template for determining the molecular structures of other compounds. The study also showed that spectrum prediction capability existed when compounds similar to that of the new chemical variant were analyzed. These principles may assist in situations in which an unfamiliar, unknown, or low spectral library match to a spectrum exists. This paper helps the analyst approach the next step of the problem, which may be to perform a peak-position search for related structures, spectral decomposition analysis, or synthesis or purchase of the deduced molecular candidate. Although other research has studied aspects of methamphetamine in detail, a full fragmentation study has not been previously reported. In addition to showing molecular structures represented by fragment peaks, mechanisms for selected processes are described. The paper also outlines an empirically derived procedure for easily determining by simple spectral peak pattern recognition of the geometry of dimethyl- or ethyl-substituted immonium ions. 1 table, 10 figures, and 34 references